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(-) Description

Title :  BSUCP CRYSTAL STRUCTURE
 
Authors :  M. M. Lee, C. E. Isaza, J. D. White, R. P. -Y. Chen, G. F. -C. Liang, H. T. - F. He, S. I. Chan, M. K. Chan
Date :  05 Jun 09  (Deposition) - 30 Jun 09  (Release) - 13 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Hydrolase, Metal-Binding, Metalloprotease, Protease, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Lee, C. E. Isaza, J. D. White, R. P. Chen, G. F. Liang, H. T. He, S. I. Chan, M. K. Chan
Insight Into The Substrate Length Restriction Of M32 Carboxypeptidases: Characterization Of Two Distinct Subfamilies.
Proteins V. 77 647 2009
PubMed-ID: 19544567  |  Reference-DOI: 10.1002/PROT.22478
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACILLUS SUBTILIS M32 CARBOXYPEPTIDASE
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-DE3
    Expression System Taxid: 562
    Expression System Vector Type: PET-28B(+)
    Gene: BSU22080, YPWA
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2F1Ligand/IonFLUORIDE ION
3PO42Ligand/IonPHOSPHATE ION
4ZN7Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2F-1Ligand/IonFLUORIDE ION
3PO42Ligand/IonPHOSPHATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2F-1Ligand/IonFLUORIDE ION
3PO44Ligand/IonPHOSPHATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:265 , HIS A:269 , GLU A:295 , PO4 A:503BINDING SITE FOR RESIDUE ZN A 502
02AC2SOFTWAREPRO A:235 , HIS A:265 , GLU A:266 , HIS A:269 , GLU A:295 , TYR A:420 , ZN A:502 , HOH A:556BINDING SITE FOR RESIDUE PO4 A 503
03AC3SOFTWAREHIS A:28 , GLU A:114 , CL A:505 , CL A:509BINDING SITE FOR RESIDUE ZN A 504
04AC4SOFTWAREZN A:504BINDING SITE FOR RESIDUE CL A 505
05AC5SOFTWAREGLU A:114 , ZN A:504BINDING SITE FOR RESIDUE CL A 509
06AC6SOFTWAREHIS A:310 , CL A:507 , ZN A:508 , CL A:510BINDING SITE FOR RESIDUE ZN A 506
07AC7SOFTWARELYS A:309 , HIS A:310 , ZN A:506 , ZN A:508BINDING SITE FOR RESIDUE CL A 507
08AC8SOFTWAREHIS A:310 , ASP A:442 , ZN A:506 , ZN A:508BINDING SITE FOR RESIDUE CL A 510
09AC9SOFTWARELYS A:309 , HIS A:310 , GLU A:446 , ZN A:506 , CL A:507 , CL A:510BINDING SITE FOR RESIDUE ZN A 508
10BC1SOFTWAREHIS B:265 , HIS B:269 , GLU B:295 , SER B:298 , PO4 B:503BINDING SITE FOR RESIDUE ZN B 502
11BC2SOFTWAREPRO B:235 , HIS B:265 , GLU B:266 , HIS B:269 , GLU B:295 , TYR B:420 , ZN B:502BINDING SITE FOR RESIDUE PO4 B 503
12BC3SOFTWAREHIS B:28 , GLU B:114 , CL B:505 , CL B:506BINDING SITE FOR RESIDUE ZN B 504
13BC4SOFTWAREZN B:504BINDING SITE FOR RESIDUE CL B 505
14BC5SOFTWAREHIS B:28 , GLU B:114 , ZN B:504BINDING SITE FOR RESIDUE CL B 506
15BC6SOFTWAREGLU B:449 , HIS B:451 , CL B:508BINDING SITE FOR RESIDUE ZN B 507
16BC7SOFTWAREZN B:507BINDING SITE FOR RESIDUE CL B 508
17BC8SOFTWARETHR A:33 , HOH A:554 , HOH A:610 , ARG B:228BINDING SITE FOR RESIDUE F B 509

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HQ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HQ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HQ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HQ2)

(-) Exons   (0, 0)

(no "Exon" information available for 3HQ2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:496
 aligned with CBP1_BACSU | P50848 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:496
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494      
           CBP1_BACSU     5 TYEKEFFDLLKRISHYSEAVALMHWDSRTGAPKNGSEDRAESIGQLSTDIFNIQTSDRMKELIDVLYERFDDLSEDTKKAVELAKKEYEENKKIPEAEYKEYVILCSKAETAWEEAKGKSDFSLFSPYLEQLIEFNKRFITYWGYQEHPYDALLDLFEPGVTVKVLDQLFAELKEAIIPLVKQVTASGNKPDTSFITKAFPKEKQKELSLYFLQELGYDFDGGRLDETVHPFATTLNRGDVRVTTRYDEKDFRTAIFGTIHECGHAIYEQNIDEALSGTNLSDGASMGIHESQSLFYENFIGRNKHFWTPYYKKIQEASPVQFKDISLDDFVRAINESKPSFIRVEADELTYPLHIIIRYEIEKAIFSNEVSVEDLPSLWNQKYQDYLGITPQTDAEGILQDVHWAGGDFGYFPSYALGYMYAAQLKQKMLEDLPEFDALLERGEFHPIKQWLTEKVHIHGKRKKPLDIIKDATGEELNVRYLIDYLSNKYSNLYL 500
               SCOP domains d3hq2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh........eee.....eeeee..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhhhh.hhhhhhhhh.......hhhhhhhhhh......hhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hq2 A   5 TYEKEFFDLLKRISHYSEAVALMHWDSRTGAPKNGSEDRAESIGQLSTDIFNIQTSDRMKELIDVLYERFDDLSEDTKKAVELAKKEYEENKKIPEAEYKEYVILCSKAETAWEEAKGKSDFSLFSPYLEQLIEFNKRFITYWGYQEHPYDALLDLFEPGVTVKVLDQLFAELKEAIIPLVKQVTASGNKPDTSFITKAFPKEKQKELSLYFLQELGYDFDGGRLDETVHPFATTLNRGDVRVTTRYDEKDFRTAIFGTIHECGHAIYEQNIDEALSGTNLSDGASMGIHESQSLFYENFIGRNKHFWTPYYKKIQEASPVQFKDISLDDFVRAINESKPSFIRVEADELTYPLHIIIRYEIEKAIFSNEVSVEDLPSLWNQKYQDYLGITPQTDAEGILQDVHWAGGDFGYFPSYALGYMYAAQLKQKMLEDLPEFDALLERGEFHPIKQWLTEKVHIHGKRKKPLDIIKDATGEELNVRYLIDYLSNKYSNLYL 500
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494      


Chain B from PDB  Type:PROTEIN  Length:497
 aligned with CBP1_BACSU | P50848 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:497
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       
           CBP1_BACSU     4 HTYEKEFFDLLKRISHYSEAVALMHWDSRTGAPKNGSEDRAESIGQLSTDIFNIQTSDRMKELIDVLYERFDDLSEDTKKAVELAKKEYEENKKIPEAEYKEYVILCSKAETAWEEAKGKSDFSLFSPYLEQLIEFNKRFITYWGYQEHPYDALLDLFEPGVTVKVLDQLFAELKEAIIPLVKQVTASGNKPDTSFITKAFPKEKQKELSLYFLQELGYDFDGGRLDETVHPFATTLNRGDVRVTTRYDEKDFRTAIFGTIHECGHAIYEQNIDEALSGTNLSDGASMGIHESQSLFYENFIGRNKHFWTPYYKKIQEASPVQFKDISLDDFVRAINESKPSFIRVEADELTYPLHIIIRYEIEKAIFSNEVSVEDLPSLWNQKYQDYLGITPQTDAEGILQDVHWAGGDFGYFPSYALGYMYAAQLKQKMLEDLPEFDALLERGEFHPIKQWLTEKVHIHGKRKKPLDIIKDATGEELNVRYLIDYLSNKYSNLYL 500
               SCOP domains d3hq2b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhh.eee.....eeeee..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........hhhhh..........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hq2 B   4 HTYEKEFFDLLKRISHYSEAVALMHWDSRTGAPKNGSEDRAESIGQLSTDIFNIQTSDRMKELIDVLYERFDDLSEDTKKAVELAKKEYEENKKIPEAEYKEYVILCSKAETAWEEAKGKSDFSLFSPYLEQLIEFNKRFITYWGYQEHPYDALLDLFEPGVTVKVLDQLFAELKEAIIPLVKQVTASGNKPDTSFITKAFPKEKQKELSLYFLQELGYDFDGGRLDETVHPFATTLNRGDVRVTTRYDEKDFRTAIFGTIHECGHAIYEQNIDEALSGTNLSDGASMGIHESQSLFYENFIGRNKHFWTPYYKKIQEASPVQFKDISLDDFVRAINESKPSFIRVEADELTYPLHIIIRYEIEKAIFSNEVSVEDLPSLWNQKYQDYLGITPQTDAEGILQDVHWAGGDFGYFPSYALGYMYAAQLKQKMLEDLPEFDALLERGEFHPIKQWLTEKVHIHGKRKKPLDIIKDATGEELNVRYLIDYLSNKYSNLYL 500
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HQ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HQ2)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CBP1_BACSU | P50848)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004181    metallocarboxypeptidase activity    Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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